In 1994 we discovered that yeast can have prions, infectious proteins analogous to the transmissible spongiform encephalopathies of mammals. We showed that the non-Mendelian genetic element, URE3, is a prion of the Ure2 protein, and that PSI+ is a prion of Sup35p (1,2). These prions are amyloids of the respective proteins (3). Our discovery showed that proteins can be genes. Unexpectedly, shuffling the prion domain amino acid sequence of Ure2p or Sup35p did not alter the ability of these domains to support prion formation, suggesting that the amyloid structure is parallel in-register (4). We have shown by solid-state NMR (with Rob Tycko of NIDDK) that the amyloids of Ure2p, Sup35p and Rnq1p are indeed folded in-register parallel beta sheets (5-7). This architecture explains how a given protein sequence can template its structure, and thus how a protein can act as a gene (8). We have used singly- 13C-labeled Sup35NM molecules to confirm our folded parallel in-register beta sheet model of the infectious prion amyloid of Sup35p and to suggest the locations of some of the folds (9). URE3 and PSI+ prion-forming ability of Ure2p and Sup35p are scattered among yeast and fungal species (10, 11). Moreover, the prion (amyloid)-forming parts of Ure2p and Sup35p have normal functions, suggesting that neither PSI+ - forming nor URE3 - forming ability are conserved, but are rare side effects of domains conserved for normal functions. We find that PSI+ and URE3 are rare in wild strains, though they would be common if they were advantageous (12). We used population genetics to show that cells carrying even the mildest forms of the yeast prions PSI+, URE3 or PIN+ have a >1% growth/survival detriment (13). About 10% of wild strains carry the PIN+ prion (12), but PIN+ arises only very rarely. We find that the presence of PIN+ in wild strains is associated with a history, detected from genome sequences, of outcross mating, indicating that PIN+ is an infectious disease, rather than becoming widespread as a result of conferring an advantage on the host cells (14). We showed that PSI+ and URE3 are most often toxic or even lethal, the PSI+ lethality being caused by sequestration in amyloid of the essential Sup35 protein (15). Most variants of the URE3 prion cause extremely slow growth, although deletion of the URE2 gene in these strains did not slow growth (15). This toxic URE3 must be a due to a pathogenic amyloid, confirming the pathologic nature of the yeast prions PSI+ and URE3. Understanding their mechanisms of pathogenesis may be useful in understanding human amyloidoses. We sequenced the SUP35 genes of 55 wild S. cerevisiae isolates, finding three groups of common polymorphs (16). PSI+ transmission between polymorphs is largely blocked, suggesting that these changes are selected to protect yeast from the detrimental effects of the prion (16). Indeed, the rate of evolutionary change of the prion domain is much faster than that of the remainder of the molecule suggesting that selection for resistance to infection by prions is driving change in the prion domain. We find that the rare wild PSI+ variants are sensitive to these blocks as well, supporting this interpretation (17). We find that transmission efficiency of PSI+ from a strain with one Sup35p polymorph to one with another polymorph is highly dependent on the variant of PSI+ (16, 17). Using this transmission frequency as a marker for different prion variants, we demonstrated segregation (separation) of prion variants during growth of the cells under non-selective conditions, and the generation of new variants, presumably due to occasional mis-templating of the amyloid (17). Data suggestive of this prion cloud phenomenon in mammalian prions has been published and it is likely to apply as well to the common human amyloid diseases. Our studies of prion inheritance, mutation and pathogenesis indicate that prions are inherited and selected at two levels: a) the DNA sequence of the prion protein determines the range of possible prion variants and the normal function of the protein and b) the individual prion variant determines the effects of prion function on the cell (18). We found that overproduction of Btn2p or Cur1p could cure the URE3 prion (19), and that in the process of curing URE3, Ure2p aggregates co-localized with Btn2p in a single locus (19). We now find that the large majority of URE3 variants isolated in a btn2 cur1 mutant are cured by restoring just the normal level of Btn2p and Cur1p (20). Moreover, we find that it is specifically URE3 variants of low seed number that are cured by normal levels of these proteins (20). We propose that Btn2p collects prion aggregates, increasing the likelihood that one of the progeny cells will not get any prion seeds and so be cured. We showed that overproduced Hsp42, a small heat shock protein, also cures URE3, and Hsp42 is necessary for curing of URE3 by overproduced Btn2p (20). Btn2p, Cur1p and Hsp42 work together at normal levels to cure URE3 prions that arise. They comprise an anti-prion system. Btn2p has low level homology with mammalian HOOK proteins which are involved in transporting aggregates and organelles around the cell, including formation of the mammalian 'aggresome'. The disaggregating chaperone Hsp104 is necessary for the propagation of nearly all amyloid-based yeast prions, but can cure the PSI+ prion if overexpressed. Mutants in the Hsp104 N-terminal domain, such as T160M can propagate PSI+ normally, but cannot cure it even if overexpressed. We found that most PSI+ variants isolated in the Hsp104 T160M mutant are cured by restoration of normal levels of w.t. Hsp104, showing that this activity is an antiprion system that works under normal circumstances to deminish the risk of prion pathology (21). 1. Wickner RB (1994) URE3 as an altered URE2 protein: evidence for a prion analog in S. cerevisiae. Science 264: 566 - 569. 2. Masison DC & Wickner RB (1995) Science 270: 93 - 95. 3. Wickner RB, Edskes HK, Ross ED, Pierce MM, Baxa U, Brachmann A & Shewmaker F (2004) Ann. Rev. Genetics 38: 681-707. 4. Ross ED, Minton AP & Wickner RB (2005) Nature Cell Biol. 7: 1039-1044. 5. Shewmaker F, Wickner RB & Tycko R (2006) Proc. Natl. Acad. Sci. USA 103: 19754 - 19759. 6. Baxa U, Wickner RB, Steven AC, Anderson D, Marekov L, Yau W-M & Tycko R (2007) Biochemistry 46: 13149 - 13162. 7. Wickner RB, Dyda F & Tycko R (2008) Proc Natl Acad Sci U S A 105: 2403 - 2408. 8. Wickner RB, Edskes HK, Shewmaker F, Nakayashiki T 2007 Nat. Rev. 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